Problem of Grandfathering clause in filling returns

We have filled our return where long term capital gain was mentioned as per provisions of Grandfathering clause. Now we have received this message :- 

"There is inconsistency in the LTCG amounts /Totals entered in schedule CG OR Taxpayer is claiming deductions u/s 54 which are more than the amounts allowable as per the respective sections."

Can anyone explain what should we do to solve this query ??